pangenome {FindMyFriends} | R Documentation

## Construct a pangenome from fasta files

### Description

This function constructs an initial pangenome object from a set of fasta files. Note that the actual pangenome is not calculated here. As such this function mainly sets everything up before beginning the more lengthly pangenome calculation.

### Usage

    pangenome(paths, translated, geneLocation = NULL, lowMem = FALSE, ...)

### Arguments

`paths` | A character vector with location of fasta files
`translated` | A boolean indicating if the fasta files contain amino acid sequences
`geneLocation` | A function, string or dataframe. If it is a data.frame it should contain the columns 'contig', 'start', 'end' and 'strand' with a row for each gene. If it is a function it should take the name (fasta description) for each gene and output a data.frame similar to described above. If it is a string it should specify the format of the gene names. Currently only 'prodigal' is supported.
`lowMem` | Boolean. Should FindMyFriends avoid storing sequences in memory.
`...` | Additional defaults to set on the object

### Value

A pgVirtual subclass object depending on geneLocation and lowMem.

geneLocation | lowMem | Resulting class
NULL | FALSE | `pgFull`
NULL | TRUE | `pgLM`
!NULL | FALSE | `pgFullLoc`
!NULL | TRUE | `pgLMLoc`

### Examples

    location <- tempdir()
    unzip(system.file('extdata', 'Mycoplasma.zip', package='FindMyFriends'),
          exdir=location)
    genomeFiles <- list.files(location, full.names=TRUE, pattern='*.fasta')

    # Create pgFull
    pangenome(genomeFiles, TRUE)

    # Create pgFullLoc
    pangenome(genomeFiles, TRUE, geneLocation='prodigal')

    # Create pgLM
    pangenome(genomeFiles, TRUE, lowMem=TRUE)

    # Create pgLMLoc
    pangenome(genomeFiles, TRUE, geneLocation='prodigal', lowMem=TRUE)

[Package FindMyFriends version 1.10.0 Index]